Prediction of contact residue pairs based on co-substitution between sites in protein structures.

ABSTRACT: Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints in varying degrees on each residue site. Selective constraints on residue sites are recorded in amino acid orders in homologous sequences and also in the evolutionary trace of amino acid substitutions. A challenge is to extract direct dependences between residue sites by removing phylogenetic correlations and indirect dependences through other residues within a protein or even through other molecules. Rapid growth of protein families with unknown folds requires an accurate de novo prediction method for protein structure. Recent attempts of disentangling direct from indirect dependences of amino acid types between residu

SUBMITTER: Miyazawa S 

PROVIDER: S-EPMC3546969 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature